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		<title>Visualization - Intensity plot</title>
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<h1>Intensity plot</h1>

<h2>Description</h2>
<p>

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<h4>Parameters</h4>
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	<dt>Data files</dt>
    	<dd>Selects the raw data files from where the peaks were detected</dd>
	<dt>X axis value</dt>
    	<dd>X axis display the raw data file name or the parameter defined in the "set sample parameters" window</dd>
	<dt>X axis value</dt>
    	<dd>The user can choose from peak's height, area or retention time value to display in this axis.</dd>
	<dt>Peaks</dt>
    	<dd>The user can select the peaks to use in this plot.</dd>

</dl>

<h4>Functionality</h4>
<p>
This plot is using the third part library JfreeChart for its basic functionality. 
To zoom in, drag the mouse from left to right, selecting the area to zoom. To zoom out drag the zoom from right to left.
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<p>
<img src="intensity.png">
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<p>
A tool bar on the right side of the window has a button to switch off/on the display of lines to connect the points.
<p>
<img src="intensity_lines.png">
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<p>
Optionally an error bar can be displayed indicating the standard deviation of the peak value in many samples. In order to display this bar, 
the raw data files need to be grouped. This functionality is done by setting sample parameters defined by the user. 
<p>
<img src="intensity_error.png">
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